VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Fri May 13 2016 - 09:53:36 CDT

Hi John,

Thank you for the suggestion.

I have one follow-up question. Looking through the salt bridge plugin
script, seems like the distances it prints are between the centers of the
atom selections with acidic oxygens and basic nitrogens, i.e. for ASP and
ARG, it gives the distance between the center of the two ASP oxygens and
the center of the ARG nitrogens. Is that correct? I am using VMD 1.9.2

Regards,
Chitrak.

On Thu, May 12, 2016 at 12:26 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> I would expect that you could post-process the output of the existing
> tool to achieve your desired result with some additional scripting so you
> would only accept the candidates that match your particular additional
> criteria.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, May 05, 2016 at 05:25:20PM -0400, Chitrak Gupta wrote:
> > Hi everyone,
> > Is there a way to find intermolecular salt bridges in VMD? From what I
> > understand, the plugin only does intramolecular, i.e. looks for donor
> and
> > acceptor in the same atom selection. Is it possible to look for
> donors and
> > acceptors in different atomselection?
> > Specifically, I want to find salt bridges between acidic residues and
> > choline N (from POPC lipid) and between basic residues and phosphate
> > oxygens (lipid headgroup).
> > Regards,
> > Chitrak.
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>